Methods for determining the quality of an embryo

ABSTRACT

The present invention relates generally to the fields of reproductive medicine. More specifically, the present invention relates to in vitro non invasive methods and kits for determining the quality of an embryo by determining the level of the cell free nucleic acids and/or determining the presence and/or expression level of at least one specific nucleic acid sequence in the nucleic acid extraction.

FIELD OF THE INVENTION

The present invention relates generally to the fields of reproductivemedicine. More specifically, the present invention relates to methodsand kits for determining the quality of an embryo.

BACKGROUND OF THE INVENTION

Currently, there is no reliable commercially available genetic ornon-genetic procedure for determining the quality of an embryo duringassisted reproductive technology (ART). Notably an essential issueremains to determine whether an embryo is capable of yielding viableoffspring when transferred to an appropriate uterine environment.Another important issue is to determine the genetic profiling of anembryo that will render the development of the foetus and even after ofthe child viable.

The selection of embryos with higher implantation potential is one ofthe major challenges in assisted reproductive technology (ART).Initially, multiple-embryo transfer (MET) was used to maximize pregnancyrates. However, improved embryo quality and raising multiple pregnancyrates have resulted in the decrease in the number of embryos forreplacement. Therefore, selection of the ‘best’ embryo has becomecrucial, particularly with elective single embryo transfer (SET) beingstrongly recommended. There is therefore a need to develop new objectiveapproaches for embryo selection. The classical methods to select healthyembryos under IVF and ICSI conditions are based on subjectivemorphological criteria such as fragmentation degree and the presence ofmulti-nucleation, the number and size of blastomeres, early embryoniccleavage (Ebner et al., 2003; Fenwick et al., 2002). However, moststudies suggest that embryos with proper morphological appearance aloneare not sufficient to predict a successful implantation. Considering thelimitation of morphologic evaluation and cytogenetic screening methods,there is now a movement toward more sophisticated, high-performancetechnologies and the emerging ‘omics’ science, such as transcriptomicsand metabolomics. These approaches focus on a variety of bodily cells aswell as embryonic culture media. An indirect and attractive approach forpredicting embryo and pregnancy outcomes has been reported by our teamusing transcriptomic data of cumulus cells (CCs) gene expression (Assouet al., 2011; Assou et al., 2008). We observed that there was norelationship between embryo morphological aspects and the CC geneexpression profile (Assou et al., 2010). Other studies reported thatmetabolomic profile of spent culture media by Raman or near-infrared(NIR) spectroscopy correlates with reproductive potential of individualembryos (Seli et al., 2007; Vergouw et al., 2008). They showed also thatmetabolomic profiling of culture media from embryos was independent ofmorphology.

Another major cause of reduced implantation rate is poor genetic qualityof the implanted embryo. For example, most embryonic wastage and lossare caused by aneuploidies (chromosome number abnormalities) that arelethal and occur in approximately 60% of all spontaneous abortions andstill births. Other genetic abnormalities include chromosomalaneuploidy, amplification, translocation, insertion/deletion, inversion,short tandem repeat polymorphisms, microsatellite polymorphisms, singlenucleotide polymorphisms (SNPs), and other structural abnormalities.Genetic abnormalities can cause many phenotypic diseases and some areeven lethal. If genetic abnormalities occur in embryos, many types ofprenatal conditions and congenital diseases are likely to develop.Screening these abnormalities by preimplantation genetic diagnosis (PGD)is very important to ensure a structurally normal embryo selection andviable implantation. However, current methods are invasive may causeprejudice to the embryo.

It was reported that cell free DNA may be detected in biological fluidssuch as blood, ascite, urine, amniotic fluid, feces, saliva orcerebrospinal fluids. Various nucleic acids such as DNA, RNA, miRNA wereindeed isolated and detected in cell free form. cfDNA was founddetectable amount in healthy subjects as well as, in greater amount, insome pathological disorders (cancer, myocardial infarction, autoimmunedisease, sepsis, trauma, . . . ) or specific physiological state(intense effort, . . . ). The mechanisms of release of cfDNA are verypoorly known, but it has been suggested that necrosis, apoptosis,phagocytosis or active release might be implicated. CfDNA analysis is anarea of active investigation in the diagnostic field especially in twoareas is subjected to high scrutiny at this time. However, detection ofcfDNA has not yet been investigated for determining the quality of anembryo.

SUMMARY OF THE INVENTION

The present invention is based on the dramatic discovery of the presenceof amounts of cell free nucleic acids in the culture medium where theembryo is grown under in vitro fertilization conditions. The inventorsdemonstrate that the level of said cell free nucleic acids in theculture medium is informative about the ability of the embryo to giverise to a pregnancy. Moreover, the inventors demonstrate that theanalysis of said cell free nucleic acids make the detection andexpression of a specific sequence gene expression possible and pave theway for the development of a non-invasive method for the geneticprofiling of an embryo.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to an in vitro non invasive method fordetermining the quality of an embryo comprising the steps consisting ofi) providing a sample of the culture medium where the embryo is grown,ii) extracting the cell free nucleic acids from the sample and iii)determining the level of the cell free nucleic acids in the nucleic acidextraction and/or determining the presence and/or expression level of atleast one specific nucleic acid sequence in the nucleic acid extraction.

As used herein the term “embryo” has its general meaning in the art andrefers to a fertilized oocyte or zygote. The term “embryo” also refersto cells in all stages of development from a fertilized oocyte or zygoteup to the 5 or 6 days (blastocyst stage). Said fertilization mayintervene under a classical in vitro fertilization (cIVF) conditions orunder an intracytoplasmic sperm injection (ICSI) procedure. Examples ofembryos that may be assessed by the methods of the invention include1-cell embryos (also referred to as zygotes), 2-cells embryo, 3-cellsembryo, 4-cells embryo, 5-cells embryo, 6-cells embryo, 8-cells embryo,etc. typically up to and including 16-cells embryo, any of which may bederived by any convenient manner, e.g. from an oocyte that has maturedin vivo or from an oocyte that has matured in vitro. As used herein, theterm “blastocyst” refers to the structure formed in the earlyembryogenesis of mammals, after the formation of the morula. Itpossesses an inner cell mass (ICM), or embryoblast, which subsequentlyforms the embryo, and an outer layer of cells, or trophoblast, whichlater forms the placenta. The trophoblast surrounds the inner cell massand a fluid-filled blastocyst cavity known as the blastocoele. The humanblastocyst comprises 70-100 cells. Blastocyst formation begins at day5/6 after fertilization in humans.

According to the invention, the oocyte may result from a natural cycle,a modified natural cycle or a stimulated cycle for cIVF or ICSI. Theterm “natural cycle” refers to the natural cycle by which the female orwoman produces an oocyte. The term “modified natural cycle” refers tothe process by which, the female or woman produces an oocyte or twounder a mild ovarian stimulation with GnRH antagonists associated withrecombinant FSH or hMG. The term “stimulated cycle” refers to theprocess by which a female or a woman produces one or more oocytes understimulation with GnRH agonists or antagonists associated withrecombinant FSH or hMG.

The term “classical in vitro fertilization” or “cIVF” refers to aprocess by which oocytes are fertilised by sperm outside of the body, invitro. IVF is a major treatment in infertility when in vivo conceptionhas failed. The term “intracytoplasmic sperm injection” or “ICSI” refersto an in vitro fertilization procedure in which a single sperm isinjected directly into an oocyte. This procedure is most commonly usedto overcome male infertility factors, although it may also be used whereoocytes cannot easily be penetrated by sperm, and occasionally as amethod of in vitro fertilization, especially that associated with spermdonation.

By “determining the quality of an embryo” it is meant that the method ofthe invention aims at determining whether an embryo is competent and/orbears a genetic abnormality or a specific sequence in the context of invitro fertilization. The method of the invention allows the assessmentof the ability of an embryo to perform successfully either or both interms of conferring a high pregnancy rate and/or resulting in a healthyperson. Accordingly the method of the invention is able to combinepre-implantation genetic testing and selection of the best embryo thatis able to give rise to pregnancy.

The term “competent embryo” refers to an embryo with a high implantationrate leading to pregnancy. The term “high implantation rate” means thepotential of the embryo when transferred in uterus, to be implanted inthe uterine environment and to give rise to a viable fetus, which inturn develops into a viable offspring absent of a procedure or eventthat terminates said pregnancy.

As used herein the term “genetic abnormality” refers to any event thatcan exist in the genome of an individual (i.e. an embryo) that can giverise to cause a phenotypic disease and lethality. Genetic abnormalitiesinclude but are not limited to aneuploidy, translocation, gene/locusamplification, insertions, deletions, reversions, short tandem repeat(STR) polymorphisms, microsatellite polymorphisms, single nucleotidepolymorphisms (SNPs), single genetic mutations responsible for inheriteddiseases, or a combination thereof. In particular, any geneticallytransmissible disease may be detected according to the present method.For example genetic alteration can include known alterations in one ormore of the genes: CFTR, Factor VIII (F8 gene), beta globin,hemachromatosis, G6PD, neurofibromatosis, GAPDH, beta amyloid, andpyruvate kinase. The sequences and common mutations (e.g., singlenucleotide polymorphisms or SNPs) of the genes are known. Other geneticabnormalities may be detected, such as those involving a sequence whichis deleted in a human chromosome, is moved in a translocation orinversion, or is duplicated in a chromosome duplication, wherein saidsequence is characterized in a known genetic disorder in the fetalgenetic material. For example chromosome aneuploidy, such as Downsyndrome (or trisomy 21), Edwards syndrome (trisomy 18), Patau syndrome(trisomy 13), Turner Syndrome (45X0) Klinefelter's syndrome (a male with2× chromosomes), Prader-Willi syndrome, and DiGeorge syndrome. A listingof known genetic abnormalities may be found in the OMIM database(http://omim.org/).

The method of the invention is applicable preferably to women but intheory may be applicable to other mammals (e.g., primates, dogs, cats,pigs, cows, mouse . . . ).

As used herein the term “nucleic acid” has its general meaning in theart and refers to refers to a coding or non coding nucleic sequence.Nucleic acids include DNA (deoxyribonucleic acid) and RNA (ribonucleicacid). Example of nucleic acid thus include but are not limited to DNA,mRNA, tRNA, rRNA, tmRNA, miRNA, piRNA, snoRNA, and snRNA. According tothe invention, the nucleic acid may originate form the nucleus of theembryo or for the mitochondrial compartment of the embryo. By “cell freenucleic acid” it is meant that the nucleic acid is released by theembryo and present in the culture medium wherein the embryo is grownafter in vitro fertilization or intracytoplasmic sperm injection (ICSI).

In a particular embodiment, sample is prepared when the embryo hasreached the balstocyst stage corresponding to day 5 or 6 of the embryodevelopment. Any methods well known in the art may be used for preparinga sample of the culture medium where the embryo was grown after in vitrofertilization or intracytoplasmic sperm injection (ICSI). One essentialfeature of the invention is that the embryo remains viable duringpreparation of the sample. No lytic enzyme or chemical reagents-basedlysis solution are used to maintain the integrity of the embryo. Themethod of the invention is a perfect non-invasive method and only reliesto the fact that an embryo is capable to release nucleic acids in theculture medium by a mechanism not yet determined.

Any methods well known in the art may be used by the skilled artisan inthe art for extracting the free cell nucleic acid from the preparedsample. For example, the method described in the example may be used.

In a particular embodiment the method of the invention comprises thesteps consisting of i) determining the level of the nucleic acid in thenucleic acid extraction, ii) comparing the level determined at step i)with a reference value, and iii) concluding that the embryo is competentwhen the level determined at step i) is lower than the reference value.

Determination of the level of the nucleic acid can be performed by avariety of techniques well known in the art. In a particular embodiment,quantitative PCR may be performed for determining the level of DNA suchas described in El Messaoudi et al., 2013; Mouliere et al., 2013;Thierry et al., 2013 and WO2012/028746. In particular, the determinationof the level of the nucleic acid may be performed as described in theexample.

In a particular embodiment, the reference value consists in the level ofthe nucleic acids determined in an embryo culture medium at day 3 ofembryo development. Accordingly, the decrease of the level between day 3of embryo development and day 5 or 6 (blastocyst stage) indicates thatthe embryo is competent

In a particular embodiment, the reference value is a threshold value ora cut-off value that can be determined experimentally, empirically, ortheoretically. A threshold value can also be arbitrarily selected basedupon the existing experimental and/or clinical conditions, as would berecognized by a person of ordinary skilled in the art. The thresholdvalue has to be determined in order to obtain the optimal sensitivityand specificity according to the function of the test and thebenefit/risk balance (clinical consequences of false positive and falsenegative). Typically, the optimal sensitivity and specificity (and sothe threshold value) can be determined using a Receiver OperatingCharacteristic (ROC) curve based on experimental data. Preferably, theperson skilled in the art may compare the nucleic acid levels (obtainedaccording to the method of the invention) with a defined thresholdvalue. In one embodiment of the present invention, the threshold valueis derived from the nucleic acid levels (or ratio, or score) determinedin an embryo culture mediums derived from one or more patientsundergoing IVF or ISCI. Furthermore, retrospective measurement of thenucleic acid levels (or ratio, or scores) in properly banked historicalembryo culture mediums of patients undergoing IVF or ISCI may be used inestablishing these threshold values.

In a particular embodiment the method of the invention comprises thesteps consisting of i) detecting at least one mutation in the nucleicextraction, and ii) concluding that the embryo bears a geneticabnormality when the mutation is detected.

Typical techniques for detecting a mutation in a nucleic acid inparticular DNA or mRNA include but are not limited restriction fragmentlength polymorphism, hybridisation techniques, sequencing, exonucleaseresistance, microsequencing, solid phase extension using ddNTPs,extension in solution using ddNTPs, oligonucleotide assays, methods fordetecting single nucleotide polymorphism such as dynamic allele-specifichybridisation, ligation chain reaction, mini-sequencing, DNA “chips”,allele-specific oligonucleotide hybridisation with single ordual-labelled probes merged with PCR or with molecular beacons, andothers.

Typically, mutations are detected after amplification. For instance, theisolated RNA may be subjected to coupled reverse transcription andamplification, such as reverse transcription and amplification bypolymerase chain reaction (RT-PCR), using specific oligonucleotideprimers that are specific for a mutated site or that enableamplification of a region containing the mutated site. According to afirst alternative, conditions for primer annealing may be chosen toensure specific reverse transcription (where appropriate) andamplification; so that the appearance of an amplification product be adiagnostic of the presence of a particular mutation. Otherwise, RNA maybe reverse-transcribed and amplified, or DNA may be amplified, afterwhich a mutated site may be detected in the amplified sequence byhybridization with a suitable probe or by direct sequencing, or anyother appropriate method known in the art. For instance, a cDNA obtainedfrom RNA may be cloned and sequenced to identify a mutation.

In particular sequencing represents an ideal technique that can be usedin the context of the present invention. The one skilled in the art isfamiliar with several methods for sequencing of polynucleotides. Theseinclude, but are not limited to, Sanger sequencing (also referred to asdideoxy sequencing) and various sequencing-by-synthesis (SBS) methods asreviewed by Metzger (Metzger ML 2005, Genome Research 1767), sequencingby hybridization, by ligation (for example, WO 2005/021786), bydegradation (for example, U.S. Pat. Nos. 5,622,824 and 6,140,053),nanopore sequencing. Preferably in a multiplex assay deep sequencing ispreferred. The term “deep sequencing” refers to a method of sequencing aplurality of nucleic acids in parallel. See e.g., Bentley et al, Nature2008, 456:53-59. The leading commercially available platforms producedby Roche/454 (Margulies et al., 2005a), Illumina/Solexa (Bentley et al.,2008), Life/APG (SOLiD) (McKernan et al., 2009) and Pacific Biosciences(Eid et al., 2009) may be used for deep sequencing. For example, in the454 method, the DNA to be sequenced is either fractionated and suppliedwith adaptors or segments of DNA can be PCR-amplified using primerscontaining the adaptors. The adaptors are nucleotide 25-mers requiredfor binding to the DNA Capture Beads and for annealing the emulsion PCRAmplification Primers and the Sequencing Primer. The DNA fragments aremade single stranded and are attached to DNA capture beads in a mannerthat allows only one DNA fragment to be attached to one bead. Next, theDNA containing beads are emulsified in a water-in-oil mixture resultingin microreactors containing just one bead. Within the microreactor, thefragment is PCR-amplified, resulting in a copy number of several millionper bead. After PCR, the emulsion is broken and the beads are loadedonto a pico titer plate. Each well of the pico-titer plate can containonly one bead. Sequencing enzymes are added to the wells and nucleotidesare flowed across the wells in a fixed order. The incorporation of anucleotide results in the release of a pyrophosphate, which catalyzes areaction leading to a chemiluminescent signal. This signal is recordedby a CCD camera and a software is used to translate the signals into aDNA sequence. In the Illumina method (Bentley (2008)), single stranded,adaptor-supplied fragments are attached to an optically transparentsurface and subjected to “bridge amplification”. This procedure resultsin several million clusters, each containing copies of a unique DNAfragment. DNA polymerase, primers and four labeled reversible terminatornucleotides are added and the surface is imaged by laser fluorescence todetermine the location and nature of the labels. Protecting groups arethen removed and the process is repeated for several cycles. The SOLiDprocess (Shendure (2005)) is similar to 454 sequencing, DNA fragmentsare amplified on the surface of beads. Sequencing involves cycles ofligation and detection of labeled probes. Several other techniques forhigh-throughput sequencing are currently being developed. Examples ofsuch are The Helicos system (Harris (2008)), Complete Genomics (Drmanac(2010)) and Pacific Biosciences (Lundquist (2008)). As this is anextremely rapidly developing technical field, the applicability to thepresent invention of high throughput sequencing methods will be obviousto a person skilled in the art.

In a particular embodiment the method of the invention comprises thesteps consisting of i) determining the level of at least one specificnucleic acid sequence, ii) comparing the level determined at step i)with a reference value and iii) concluding that the embryo bears agenetic abnormality when the level determined at step i) is differentfrom the reference value (i.e. lower or higher depending on the nucleicacid looked).

Determining the expression level of a nucleic acid (in particular agene, miRNA, snRNA, and snoRNA) may be assessed by any of a wide varietyof well-known methods. Typically the prepared nucleic acid can be usedin hybridization or amplification assays that include, but are notlimited to, Southern or Northern analyses, polymerase chain reactionanalyses, such as quantitative PCR (TaqMan), and probes arrays such asGeneChip™ DNA Arrays (AFF YMETRIX). Advantageously, the analysis of theexpression level of a nucleic acid involves the process of nucleic acidamplification, e. g., by RT-PCR (the experimental embodiment set forthin U.S. Pat. No. 4,683,202), ligase chain reaction (BARANY, Proc. Natl.Acad. Sci. USA, vol. 88, p: 189-193, 1991), self sustained sequencereplication (GUATELLI et al., Proc. Natl. Acad. Sci. USA, vol. 57, p:1874-1878, 1990), transcriptional amplification system (KWOH et al.,1989, Proc. Natl. Acad. Sci. USA, vol. 86, p: 1173-1177, 1989), Q-BetaReplicase (LIZARDI et al., Biol. Technology, vol. 6, p: 1197, 1988),rolling circle replication (U.S. Pat. No. 5,854,033) or any othernucleic acid amplification method, followed by the detection of theamplified molecules using techniques well known to those of skill in theart. Real-time quantitative or semi-quantitative RT-PCR is preferred. Ina particular embodiment, the determination comprises hybridizing thesample with selective reagents such as probes or primers and therebydetecting the presence, or measuring the amount of the nucleic acid.Hybridization may be performed by any suitable device, such as a plate,microtiter dish, test tube, well, glass, column, and so forth. Nucleicacids exhibiting sequence complementarity or homology to the nucleicacid of interest herein find utility as hybridization probes oramplification primers. It is understood that such nucleic acids need notbe identical, but are typically at least about 80% identical to thehomologous region of comparable size, more preferably 85% identical andeven more preferably 90-95% identical. In certain embodiments, it willbe advantageous to use nucleic acids in combination with appropriatemeans, such as a detectable label, for detecting hybridization. A widevariety of appropriate indicators are known in the art including,fluorescent, radioactive, enzymatic or other ligands (e.g.avidin/biotin). The probes and primers are “specific” to the nucleicacid they hybridize to, i.e. they preferably hybridize under highstringency hybridization conditions (corresponding to the highestmelting temperature —Tm—, e.g., 50% formamide, 5× or 6×SCC. 1×SCC is a0.15 M NaCl, 0.015 M Na-citrate). Many quantification assays arecommercially available from Qiagen (S.A. Courtaboeuf, France) or AppliedBiosystems (Foster City, USA). Expression level of the nucleic acid maybe expressed as absolute expression profile or normalized expressionprofile. Typically, expression profiles are normalized by correcting theabsolute expression profile of the nucleic acid of interest by comparingits expression to the expression of a nucleic acid that is not arelevant, e.g., a housekeeping mRNA that is constitutively expressed.Suitable mRNA for normalization include housekeeping mRNAs such as theU6, U24, U48 and S18. This normalization allows the comparison of theexpression profile in one sample, e.g., a patient sample, to anothersample, or between samples from different sources.

Probe and or primers are typically labelled with a detectable moleculeor substance, such as a fluorescent molecule, a radioactive molecule orany others labels known in the art. Labels are known in the art thatgenerally provide (either directly or indirectly) a signal. The term“labelled” is intended to encompass direct labelling of the probe andprimers by coupling (i.e., physically linking) a detectable substance aswell as indirect labeling by reactivity with another reagent that isdirectly labeled. Examples of detectable substances include but are notlimited to radioactive agents or a fluorophore (e.g. fluoresceinisothiocyanate (FITC) or phycoerythrin (PE) or Indocyanine (Cy5)).

The reference value may be determined as above described and will dependon the nucleic acid for which the determination of the expression levelis required for concluding that the embryo bears a genetic abnormalityor a nucleic acid specific sequence.

The method of the invention is particularly suitable for reaching aclinical decision. As used herein the term “clinical decision” refers toany decision to take or not take an action that has an outcome thataffects the health or survival of the embryo. In particular, in thecontext of the invention, a clinical decision refers to a decision toimplant or not the embryo of in the uterus of the patient. A clinicaldecision may also refer to a decision to conduct further testing, totake actions to mitigate an undesirable phenotype, or to take actions toprepare for the birth of a child with abnormalities. In particular themethod as above described will thus help embryologist to avoid thetransfer in uterus of embryos with a poor potential for pregnancyoutcome. The method as above described is also particularly suitable foravoiding multiple pregnancies by selecting the competent embryo able tolead to an implantation and a pregnancy and therefore fewer embryoscould be transferred at each cycle, resulting in a decreased incidenceof multiple pregnancies.

The methods of the invention are particularly suitable for enhancing thepregnancy outcome of a child with a minimum of risk of having a geneticabnormality. Accordingly the invention also relates to a method forenhancing the pregnancy outcome of a patient comprising the stepsconsisting of i) providing a plurality of embryos, ii) determining thequality of the embryo by the method according to the invention and iii)selecting the most competent embryo with the minimum risk of bearing agenetic abnormality, and iv) implanting the embryo selected at step iii)in the uterus of said patient.

The invention also relates to a kit for performing the methods as abovedescribed, wherein said kit comprises means for determining the level ofthe cell free nucleic and/or means for determining the expression levelof at least one specific nucleic acid and/or means for detecting atleast one mutation, one SNP or a specific sequence in the nucleic acidextraction. Typically, the kits include probes, primers macroarrays ormicroarrays as above described. For example, the kit may comprise a setof probes as above defined, and that may be pre-labelled. Alternatively,probes may be unlabelled and the ingredients for labelling may beincluded in the kit in separate containers. The kit may further comprisehybridization reagents or other suitably packaged reagents and materialsneeded for the particular hybridization protocol, including solid-phasematrices, if applicable, and standards. Alternatively the kit of theinvention may comprise amplification primers (e.g. stem-loop primers)that may be pre-labelled or may contain an affinity purification orattachment moiety. The kit may further comprise amplification reagentsand also other suitably packaged reagents and materials needed for theparticular amplification protocol.

The invention will be further illustrated by the following figures andexamples. However, these examples and figures should not be interpretedin any way as limiting the scope of the present invention.

FIGURES

FIG. 1: cfDNA concentrations in culture medium of several embryos fromtwo patients at Day3.

FIG. 2: cfDNA concentrations in culture medium of several embryos from 9patients at Day5/6.

FIG. 3: cfDNA concentrations in culture medium of several embryos fromtwo patients at Day3 and Day5. Dark histogram, D5/6 concentration. Clearhistogram, D3 concentration.

FIG. 4A: Difference of the cfDNA concentrations between Day3 and Day5/6respective to embryo grade. Serie 1 histograms, D3-D5/6 concentration(ng/mL cfDNA); serie 2 histograms, ranking respective to growing grade(1-10). CfDNA concentration values obtained in the serie of the embryoof the HSC patient.

FIG. 4B: cfDNA concentrations respective to embryo grade. Serie 1histograms, Day5/6 concentration (ng/mL cfDNA); serie 2 histograms,ranking respective to growing grade (1 to 10). CfDNA concentrationvalues obtained in the serie of the embryo of the HSC patient.

FIG. 5: Relationship between cfDNA in culture media and pregnancyoutcome. Histograms comparing the mean cfDNA quantity in embryo culturemedia at day 5/6 issued from positive pregnancy patients and negativepregnancy patients.

FIGS. 6A and 6B: Histograms show the microarray signal values for genesin ovary, testes, MII oocytes, day 3 embryos, day 5/6 blastocysts,trophectoderm and endometrium samples. Microarray data from MII oocytes,day 3 embryos, day 5/6 blastocysts, trophectoderm and endometriumsamples were obtained from our team and those for ovary and testessamples were obtained from the Gene Expression Omnibus (GEO) through theprovisional accession numbers (GPL570).

EXAMPLE

Material & Methods

IVF Procedure

The women underwent a gonadotropin-releasing hormone (Gn-RH) long orantagonist protocols treatment, which was followed by ovarianstimulation by hMG (human menopausal gonadotropin) or recombinantfollicle-stimulating hormone (FSH). When at least three folliclesreached a mean diameter of 17 mm under transvaginal ultrasoundexamination, 5000 IU hCG was administrated. Then, 36 h later, theoocytes were retrieved by ultrasound-guided trans-vaginal puncture.Conventional IVF or ICSI was use as indicated. Fertilization wasconfirmed 16 to 20 h after oocyte insemination or microinjection by thepresence of two distinct pronuclei under the inverted microscope+twopolar bodies. The zygotes were then placed individually into fresh 30 μldroplets of culture medium (G1.5, Vitolife, Sweden) covered with mineraloil and maintained in a tri-gas incubator, which provide a 5% oxygenenvironment. All embryos were cultured in individual droplets at alltimes. The embryos were placed into extended culture media and continueduntil day 5. G2.5 medium (Vitolife, Sweden) was used for extendedculture.

Quantification of the cfDNA in Culture Media of the Invention

Embryo Culture Media Sampling After the removal of the embryos, theculture media were placed individually into labeled cryovials and thenlabeled again with a randomly assigned accession number. The collectedspecimens were immediately frozen and stored at −80° C. A control sampleincubated under the same conditions without an embryo was alsocollected. Up to 50 μL may be sampled from the culture media.

cfDNA Extraction

For Day 3 or Day5/6 samples, initial volume of 30 μL was completed to200 μL with 170 μL of PBS 1×. For D5 samples, initial volume of 10 μLwas completed to 200 μL with 190 μL of PBS 1×. Subsequently, sampleswere either immediately handled for DNA extraction. CcfDNA was extractedfrom 200 μL of the sample using the QIAmp DNA Mini Blood Kit (Qiagen,Hilden, Germany) according to the “Blood and body fluid protocol.” DNAsamples were kept at −20° C. until use.

cfDNA Quantification by Q-PCR

The methodology and the data description were carried out according tothe MIQE guidelines.q-PCR amplifications were carried out at least induplicate in a 25-μl reaction volume on a CFX96™ real-time PCR detectionsystem using the CFX Manager™ software (Bio-Rad, Hercules, Calif.). EachPCR mixture was composed of 12.5 μl of PCR mix (Bio-Rad Supermix SYBRGreen), 2.5 μl of each amplification primer (0.3 pmol/μl), 2.5 μl ofPCR-analyzed water, and 5 μl of DNA extract. Thermal cycling consistedof three repeated steps: a 3-minute hot-start polymeraseactivation-denaturation step at 95° C. followed by 40 repeated cycles at95° C. for 10 seconds and then at 60° C. for 30 seconds. Melting curveswere obtained by increasing the temperature from 55 to 90° C. with aplate reading every 0.2° C. Serial dilutions of genomic DNA from humanplacenta cells (Sigma, Munich, Germany) were used as standard forquantification and their concentration and quality was assessed using aQubit® 2.0 Fluorometer (Life Technologies). Every Q-PCR run comprisedroutine quality negative and positive controls. Each sample was analyzedin triplicate and each assay was repeated at least once. The cfDNAconcentrations obtained were normalized to the precise concentrationusing the standard curve. The coefficient of variation of theconcentration value due to cfDNA extraction and Q-PCR analysis wascalculated as 24% from two experiments (n=12). Quantification of cfDNAin samples and realization of the standard curve were performed by usingthe primer systems described in Table 1 (KRAS B1 inv k Sense: SEQ ID NO:1; and KRAS B2 inv k Antisense: SEQ ID NO:2). Concentration valuedetermined by the test exhibit a coefficient of variation of 24%.

TABLE 1 Intplex primers used for cfDNA quantification. Intplex DirectionPrimer Sequence Tm Amplicon Species Gene Name 5′-3′ (° C.) Size (bp)Human Kras KRAS B1 CCTTGGGTTT 54.0 67 Inv k CAAGTTATATG Sense Human KrasKRAS B2 CCCTGACATA 59.4 Inv k CTCCCAAGGA Antisense

Primer Design

The sequences and characteristics of the selected primers are presentedin Table 1. The primers were designed using the Primer 3 software andall sequences were checked for self-molecular or intermolecularannealing with nucleic acid folding software (mfold and oligoAnalyzer1.2). We performed local alignment analyses with the BLAST program toconfirm the specificity of the designed primers. Oligonucleotides weresynthesized and purified on high performance liquid chromatography(HPLC) by Eurofins (Ebersberg, Germany) and quality control of theoligonucleotides was performed by matrix-assisted laser desorptionionization-time of flight (MALDI-TOF).

The Q-PCR system was designed to be able to quantify a sequence presentin two copies of the human genome. It enables the highly specific andsensitive quantification of this sequence in one allele. Higherspecificity is obtained by using Allele Specific with Blocker PCR withusing the same primers (Mouliere, 2011). This method allows fordistinguishing two sequences having only one nucleotide difference witha 0.005 mutant/WT ratio. Thus detecting and quantifying a specificsequence may correspond either at distinguishing a WT sequence versussequences with a few nucleotides difference up to only one nucleotidedifference such as in sequences with a point mutation or a SNP.Therefore the demonstration of the quantification of cfDNA in embryoculture medium as shown here, show the potential of this method todetect the presence of a single nucleotide mutation, SNP, or othergenetic alterations.

Higher concentration values may be obtained when targeting repeatedsequences in the nuclear genome such as the lyne sequence, ormitochondrial sequences.

Results

Detection of cfDNA in Embryo Culture Media

The targeted sequence has 2 copies per genome of the nucleus of diploidcell. CfDNA could significantly be detected in embryo culture media atD3 or D5/6 (FIG. 1). The test can detect down to 1.5 ng/ml medium and assuch a minimum of 2 GE copy were found in culture medium. Up to of 27ng/ml cfDNA or 36 GE was observed in D5/6 culture medium (FIG. 2). Note,those number may be relevant to the embryo development. As such thisdata reveals the possibility of the detection of the presence of aspecific DNA sequence (at the most 2 copies per diploid cell) andtherefore the potential presence of homozygous or heterozygous geneticor epigenetic alteration. CfDNA could significantly be detected in allsamples and for each patient (FIG. 2).

There are significant (1 Log) intra and inter variation between samplesbuttressing the notion that dynamics of measurement enables comparisonbetween samples (FIG. 3).

Relationship Between cfDNA and In Vitro Embryo Outcome

The relation between cfDNA content of embryo culture medium and in vitroembryo development was also investigated:

cfDNA conc. determined at D3 and D5/6 could be compared in culture mediaof eleven embryos. As shown in (FIG. 4A), the values of the differenceof the cfDNA concentration between D3 and D5/6 are growing respectivelywith the good embryo development as evaluated by morphological criteria.As presented in (FIG. 4B) cfDNA conc. values are inversely proportionalto the good embryo development. Thus, both D5/6 cfDNA conc. and D3-D5/6conc. decrease appear as a marker of in vitro embryo development.

cfDNA isolated from embryo culture media that developed into goodquality 8-cells embryo at day 3 and leading to blastocyst stage at day5/6 were selected and divided in three groups: i) cfDNA from embryo atday 3 that developed into good blastocyst quality at day 5/6 (grade 4AA,4AB or 4BA, 5AA, 5AB or 5BA) and leading to pregnancy, (ii) cfDNA fromembryo at day 3 developed into intermediary blastocyst quality at day5/6 (grade 4BB or 5 BB), (iii) cfDNA from embryo at day 3 developed intobad blastocyst quality at day 5/6 (grade 4CC or 5CC) (see table 2 forpatient HSC). The quantity of cfDNA in culture medium from embryo at day3 that developed into good blastocyst quality at day 5/6 (grade 4AA,4AB, 4BA) and leading to pregnancy was 22.16 ng/ml and 2.75 ng/ml at day3 and day 5/6 respectively (88%, decrease). The variation in the cfDNAvalue between day 3 and day 5/6 decreased to 7.55 ng/ml and 1.80 ng/ml(76%, decrease) in the intermediary grade and to 6.46 ng/ml (day 3) and3.78 (day 5/6) (41%, decrease) in the no good blastocyst grade (Table3). Interestingly, this variation is very low in the lyzed embryo 8.36ng/ml (day 3) and 5.57 (day 5/6) (33%, decrease). Additionally, cfDNAquantities in embryo culture media at day 5/6 were evaluated accordingto patient outcome. We show that cfDNA were greater in embryo culturemedia at day 5/6 from no-pregnant patients than that of pregnantpatients (FIG. 5).

cfDNA in Embryo Culture Medium could be Used to Detect Male Embryos

Genes such as TSPY1 (Testis specific protein, Y-linked 1) and RPS4Y1(Ribosomal protein S4, Y-linked 1) could be used to revealed embryo sex.This opens up an appropriate strategy for screening embryos from couplesknown to be at risk for an X-linked disease. The high-densityoligonucleotide Affymetrix HG-U133P microarray chips were used toinvestigate the expression of TSPY1 and RPS4Y1 in XX and XY samples. Ourresults reveal that TSPY1 and RPS4Y1 may prove valuable as biomarkers ofembryo sex determination by amplifying the multicops of these genes(cfDNA) in the embryo culture medium (FIGS. 6A and 6B). The methods maybe applicable to other genes localized on the chromosome Y: DDX3Y (DEAD(Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked), EIF1AY (Eukaryotictranslation) and Y chromosome gene (SRY).

TABLE 2 ICSI outcome of a patient (HSC) in relation to cfDNA detected inembryo culture media. Data generated from each mature MII oocyte(fertilization, embryo cleavage and blastocyst development) wererecorded by an embryologist according to the morphological criteria ofGardner and Schoolcraft 1999. Day 2 Day 3 Patient Day 1 BlastomereBlastomere % of Blastomere Blastomere (HSC) Fertilization numberuniformity fragmentatio number uniformity No2 Unfertilized No3fertilized 4bl Equal. Homo. 10% 7bl Equal. Homo. No4 fertilized 2PB 2PBNo5 Unfertilized No6 fertilized 4bl Unequal. ±Homo. 30% 8bl Unequal.Homo. No7 fertilized 4bl Equal. Homo. 10% 8bl Equal. Homo. No8fertilized 4bl Equal. ±Homo.  5% 8bl Equal. Homo. No9 Unfertilized No10fertilized 4bl Equal. Homo. 10% 8bl Equal. Homo. No11 Unfertilized No12fertilized 4bl Equal. Homo. 10% 8bl Equal. Heter. No13 Unfertilized No14fertilized 4bl Equal. Homo. 15% 8bl Equal. Homo. No15 fertilized 4blUnequal. Homo. 15% 6bl Unequal. Heter. No16 Unfertilized No17 fertilized4bl Unequal. ±Homo. 20% 10bl Unequal. ±Homo. No18 fertilized 4blUnequal. ±Homo. 15% 9bl Unequal. Heter. No19 Unfertilized No20fertilized 5bl Unequal. ±Homo. 10% 8bl ±Equal. Homo. No21 fertilized 3blEqual. Homo. 30% 8bl Unequal. Homo. No22 fertilized 4bl Equal. Homo. 20%8bl ±Equal. Homo. No23 fertilized 4bl Equal. Homo. 10% 8bl ±Equal.±Homo. No24 Unfertilized Drop Day 3 Drop Day 5 Day 3 ConcentrationConcentration Patient % of Day 5 Day 6 CfDNA CfDNA (HSC) fragmentatioGrade Grade Pregnancy (ng/ml) (ng/ml) No2 13.871 No3 15% 3CC 6.46 3.787No4 2.938 No5 4.73 No6 40% Lyzed 8.365 5.572 No7 30% 5BB 12.725(Frezing) No8 15% STOP 12.137 16.668 No9 4.255 No10 15% B1 other 12.6532.435 No11 33.647 No12 10% 4AB 13.542 3.81 (Frezing) No13 0.777 No14 15%B1+ 5BB 7.55 1.804 (Frezing) No15 30% B1 4BC 11.167 3.955 (Stop) No166.923 No17 20% 3CC 5CC 20.515 (Stop) No18 30% 4AC 5BA 12.07 N/A(Frezing) No19 20.968 No20 15% B1 5BB 75.392 2.28 (Frezing) No21 30% B15CC 14.219 2.81 (Stop) No22 25% 3BB 3BB 14.033 N/A (Frezing) No23 20% AAPositive 22.158 2.755 (Transfer) No24 8.41

TABLE 3 Relationship between cfDNA in culture media and in vitro embryodevelopment. Three grades of blastocysts at day 5/6 (good (AA),intermediary (BB) or bad quality (CC)) were obtained from good 8-cellembryos at day 3. The results indicate that the cfDNA variation inculture media between day 3 and day 5/6 is different according toblastocyst grade. Day 2 Day 3 Patient Day 1 Blastomere Blastomere % ofBlastomere Blastomere (HSC) Fertilization number uniformityfragmentation number uniformity No23 fertilized 4bl Equal. Homo. 10% 8bl±Equal. ±Homo. No14 fertilized 4bl Equal. Homo. 15% 8bl Equal. Homo. No3fertilized 4bl Equal. Homo. 10% 7bl Equal. Homo. Drop Day 3 Drop Day 5Day 3 Concentration Concentration Patient % of Day5 Day 6 CfDNA CfDNA(HSC) fragmentation Grade Grade Pregnancy (ng/ml) (ng/ml)) No23 20% 5AAPositive 22.168 2.755 (Transfer) No14 15% B1+ 5BB 7.55 1.804 (Frezing)No3 15% 3CC 6.46 3.787

REFERENCES

Throughout this application, various references describe the state ofthe art to which this invention pertains. The disclosures of thesereferences are hereby incorporated by reference into the presentdisclosure.

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1. A method for selecting a human embryo and subsequently implantingsaid embryo in a female undergoing in vitro fertilization, said methodcomprising the steps consisting of: i) providing a sample of the culturemedium where the embryo is grown; ii) extracting the cell free nucleicacids from the sample; iii) detecting the presence of at least onespecific nucleic acid sequence in the nucleic acid extraction; iv)selecting the embryo in view of the results obtained in step iii); andv) implanting the embryo selected in step iv) in said female.
 2. Themethod according to claim 1, wherein step iii) comprises detecting thepresence of at least one genetic alteration or genetic abnormality inthe nucleic extraction.
 3. The method according to claim 1, wherein thestep of detecting the presence of at least one specific nucleic acidsequence is performed by PCR or quantitative PCR.